alanin.params

分子动力学计算程序

remark - parameter file PARAM19 -
remark PEPTIDE GEOMETRY FROM RAMACHANDRAN ET AL BBA 359:298 (1974)
remark TORSIONS FROM HAGLER ET AL JACS 98:4600 (1976)
remark JORGENSEN NONBOND PARAMETERS JACS 103:3976-3985 WITH 1-4 RC=1.80/0.1

set echo=false end
!! - PEPTIDE GEOMETRY TO GIVE RAMACHANDRAN ET AL BBA 359:298 (1974)
!! - PEPTIDE TORSIONS FROM HAGLER ET AL JACS 98:4600 (1976)
!! - NONBONDED TERMS JORGENSEN JACS 103:3976 W/ RC1-4 = 1.80 EC1-4 = 0.1
!!  The default h-bond exponents are now 6-repul 4-attr
!! ++++++++ ATOMTYPE OS (IN METHYL ESTER) ADDED FOR CHARMM COURSE /LN ++++
!! Switched from Slater-Kirkwood to simple mixing rules - AB
!! Hbond parameters based on comparisons of dimer results with
!!   ab initio calculations. - WER  12/19/84
!! Grouping of atom types for VDW parameters - BRB 1/3/85


bond C    C      450.0  1.38!  B. R. GELIN THESIS AMIDE AND DIPEPTIDES
bond C    CH1E   405.0  1.52!  EXCEPT WHERE NOTED.  CH1E,CH2E,CH3E, AND CT
bond C    CH2E   405.0  1.52!  ALL TREATED THE SAME. UREY BRADLEY TERMS ADDED
bond C    CH3E   405.0  1.52
bond C    CR1E   450.0  1.38
bond C    CT     405.0  1.53
bond C    N      471.0  1.33
bond C    NC2    400.0  1.33!  BOND LENGTH FROM PARMFIX9 FORCE K APROXIMATE
bond C    NH1    471.0  1.33
bond C    NH2    471.0  1.33
bond C    NP     471.0  1.33
bond C    NR     471.0  1.33
bond C    O      580.0  1.23
bond C    OC     580.0  1.23!  FORCE DECREASE AND LENGTH INCREASE FROM C O
bond C    OH1    450.0  1.38!  FROM PARMFIX9 (NO VALUE IN GELIN THESIS)
bond C    OS     292.0  1.43!  FROM DEP NORMAL MODE FIT
bond CH1E CH1E   225.0  1.53
bond CH1E CH2E   225.0  1.52
bond CH1E CH3E   225.0  1.52
bond CH1E N      422.0  1.45
bond CH1E NH1    422.0  1.45
bond CH1E NH2    422.0  1.45
bond CH1E NH3    422.0  1.45
bond CH1E OH1    400.0  1.42!  FROM PARMFIX9 (NO VALUE IN GELIN THESIS)
bond CH2E CH2E   225.0  1.52
bond CH2E CH3E   225.0  1.54
bond CH2E CR1E   250.0  1.45!  FROM WARSHEL AND KARPLUS 1972 JACS 96:5612
bond CH2E N      422.0  1.45
bond CH2E NH1    422.0  1.45
bond CH2E NH2    422.0  1.45
bond CH2E NH3    422.0  1.45
bond CH2E OH1    400.0  1.42
bond CH2E S      450.0  1.81!  FROM PARMFIX9
bond CH2E SH1E   450.0  1.81
bond CH3E NH1    422.0  1.49
bond CH3E NR     422.0  1.49 ! FOR NETROPSIN
bond CH3E S      450.0  1.77!  FROM PARMFIX9
bond CH3E OS     292.0  1.38!  FROM DEP NORMAL MODE FIT
bond CM   OM    1115.0  1.128!  FROM CAUGHEY ET AL(1978),CARBON MONOXIDE
bond CR1E CR1E   450.0  1.38
bond CR1E NH1    450.0  1.305
bond CR1E NR     450.0  1.305
bond CT   CT     200.0  1.53
bond CT   N      422.0  1.45
bond CT   NC2    422.0  1.45
bond CT   NH1    422.0  1.45
bond CT   NH2    422.0  1.45
bond CT   NH3    422.0  1.45
bond CT   OH1    400.0  1.42
bond CT   S      450.0  1.81
!bond FE   CM     258.0  1.79!   FROM KROEKER ET AL(JCP:72:4846)
!bond FE   NP     500.0  2.09
!bond FE   NR      65.0  1.98!   FROM NAGAI ET AL(1980)
!bond FE   OM     250.0  1.8!    JUST A GUESS.
bond H    NH1    405.0  0.98!  GELIN AND IR STRETCH 3200 CM 1
bond H    NH2    405.0  0.98
bond H    OH1    450.0  0.96!  FROM IR STRETCH 3400 CM 1
bond HA   C      350.0  1.08
bond HA   CT     300.0  1.08
bond HC   NC2    405.0  1.00
bond HC   NH1    405.0  0.98
bond HC   NH3    405.0  1.04
bond OC   S      400.0  1.43
bond OM   OM     600.0  1.23!   STRETCHING CONSTANT JUST A GUESS.
bond S    S      500.0  2.02


angle C    C    C       70.0 106.5!  FROM B. R. GELIN THESIS WITH HARMONIC
angle C    C    CH2E    65.0 126.5!  PART OF F TERMS INCORPORATED. ATOMS
angle C    C    CH3E    65.0 126.5!  WITH EXTENDED H COMPENSATED FOR LACK
angle C    C    CR1E    70.0 122.5!  OF H ANGLES.
angle C    C    CT      70.0 126.5
angle C    C    HA      40.0 120.0!  AMIDE PARAMETERS FIT BY LEAST SQUARES
angle C    C    NH1     65.0 109.0!  TO N-METHYL ACETAMIDE VIBRATIONS.
angle C    C    NP      65.0 112.5!  MINIMIZATION OF N-METHYL ACETAMIDE.
angle C    C    NR      65.0 112.5
angle C    C    OH1     65.0 119.0
angle C    C    O       65.0 119.0 ! FOR NETROPSIN
angle CH1E C    N       20.0 117.5
angle CH1E C    NH1     20.0 117.5
angle CH1E C    O       85.0 121.5
angle CH1E C    OC      85.0 117.5
angle CH1E C    OH1     85.0 120.0
angle CH2E C    CR1E    70.0 121.5
angle CH2E C    N       20.0 117.5
angle CH2E C    NH1     20.0 117.5
angle CH2E C    NH2     20.0 117.5
angle CH2E C    NC2     20.0 117.5 ! FOR NETROPSIN
angle CH2E C    NR      60.0 116.0
angle CH2E C    O       85.0 121.6
angle CH2E C    OC      85.0 118.5
angle CH2E C    OH1     85.0 120.0
angle CH3E C    N       20.0 117.5
angle CH3E C    NH1     20.0 117.5
angle CH3E C    O       85.0 121.5
angle CR1E C    CR1E    65.0 120.5
angle CR1E C    NH1     65.0 110.5! USED ONLY IN HIS, NOT IT TRP
angle CR1E C    NP      65.0 122.5
angle CR1E C    NR      65.0 122.5
angle CR1E C    OH1     65.0 119.0
angle CT   C    N       20.0 117.5
angle CT   C    NH1     20.0 117.5
angle CT   C    NH2     20.0 117.5
angle CT   C    O       85.0 121.5
angle CT   C    OC      85.0 118.5
angle CT   C    OH1     85.0 120.0
angle HA   C    NH1     40.0 120.0
angle HA   C    NH2     40.0 120.0
angle HA   C    NR      40.0 120.0
angle HA   C    O       85.0 121.5
angle N    C    O       85.0 121.0
angle NC2  C    NC2     70.0 120.0
angle NC2  C    NH1     70.0 120.0
angle NH1  C    NR      70.0 120.0
angle NH1  C    O       65.0 121.0
angle NH2  C    O       65.0 121.0
angle O    C    OH1     85.0 120.0
angle OC   C    OC      85.0 122.5
angle OS   C    CH1E    70.0 125.3! FROM PARDNA10
angle OS   C    CH2E    70.0 125.3!   - " -
angle OS   C    O       70.0 120.0!   - " -
angle C    CH1E CH1E    70.0 110.0
angle C    CH1E CH2E    70.0 109.5
angle C    CH1E CH3E    70.0 106.5
angle C    CH1E N       45.0 111.6
angle C    CH1E NH1     45.0 111.6
angle C    CH1E NH2     45.0 111.6
angle C    CH1E NH3     45.0 111.6
angle CH1E CH1E CH2E    45.0 112.5
angle CH1E CH1E CH3E    45.0 111.0
angle CH1E CH1E NH1     50.0 110.0
angle CH1E CH1E NH2     50.0 109.5
angle CH1E CH1E NH3     50.0 107.5
angle CH1E CH1E OH1     50.0 104.5
angle CH2E CH1E CH3E    50.0 111.5
angle CH2E CH1E N       65.0 104.0
angle CH2E CH1E NH1     65.0 110.0
angle CH2E CH1E NH2     65.0 110.0
angle CH2E CH1E NH3     65.0 110.0
angle CH3E CH1E CH3E    50.0 111.0
angle CH3E CH1E NH1     65.0 108.5
angle CH3E CH1E NH2     65.0 109.5
angle CH3E CH1E NH3     65.0 109.5
angle CH3E CH1E OH1     60.0 110.5
angle C    CH2E CH1E    70.0 112.5
angle C    CH2E CH2E    70.0 113.0
angle C    CH2E NH1     70.0 111.6
angle C    CH2E NH2     70.0 111.6
angle C    CH2E NH3     70.0 111.6
angle CH1E CH2E CH1E    45.0 117.0
angle CH1E CH2E CH2E    45.0 112.5
angle CH1E CH2E CH3E    45.0 113.0
angle CH1E CH2E OH1     45.0 111.0
angle CH3E CH2E OH1     45.0 111.0
angle CH1E CH2E S       50.0 112.5
angle CH1E CH2E SH1E    50.0 112.5
angle CH2E CH2E CH2E    45.0 110.0
angle CH2E CH2E CH3E    45.0 111.0
angle CH2E CH2E N       65.0 105.0
angle CH2E CH2E NH1     65.0 111.0
angle CH2E CH2E NH2     65.0 109.5
angle CH2E CH2E NH3     65.0 110.5
angle CH2E CH2E S       50.0 112.5
angle C    CR1E C       90.0 126.5
angle C    CR1E CH2E    90.0 122.0
angle C    CR1E CR1E    90.0 119.0
angle C    CR1E NH1     90.0 109.5
angle C    CR1E NR      90.0 106.5
angle CR1E CR1E CR1E    90.0 120.5
angle NH1  CR1E NH1     70.0 109.0
angle NH1  CR1E NR      70.0 109.0
angle C    CT   CT      70.0 109.5
angle C    CT   HA      70.0 109.5
angle C    CT   N       70.0 111.6
angle C    CT   NH1     70.0 111.6
angle C    CT   NH2     70.0 111.6
angle C    CT   NH3     70.0 111.6
angle CT   CT   CT      45.0 111.00
angle CT   CT   HA      40.0 109.50
angle CT   CT   N       65.0 105.00
angle CT   CT   NC2     65.0 110.00
angle CT   CT   NH1     65.0 110.00
angle CT   CT   NH2     65.0 110.00
angle CT   CT   NH3     65.0 110.00
angle CT   CT   OH1     50.0 109.50